def leaveOneOutCrossValidation(radiographs):
print("\nSTARTING LEAVE ONE OUT CROSS VALIDATION.\n")
accuracy = 0
precision = 0
recall = 0
for i in range(len(radiographs)):
trainSet = radiographs[:i] + radiographs[i + 1:]
testSet = [radiographs[i]]
with util.Timer("Building initialization active shape models, leaving radiograph {} out".format(i)):
initModels = InitializationModel.buildModels(trainSet, PCAComponents, sampleAmount)
with util.Timer("Building tooth active shape models, leaving radiograph {} out".format(i)):
models = ToothModel.buildModels(trainSet, PCAComponents, sampleAmount)
with util.Timer("Generating segmentation masks and comparing to ground truth".format(i)):
gen = MaskGenerator(testSet[0], models, initModels)
acc, prec, rec = gen.doSearchAndCompareSegmentations()
print()
accuracy += acc
precision += prec
recall += rec
accuracy /= len(radiographs)
precision /= len(radiographs)
recall /= len(radiographs)
print("Averaged results after LOO cross-validation:")
print("Accuracy = {:.2f}%, Precision = {:.2f}%, Recall = {:.2f}%"
.format(accuracy * 100, precision * 100, recall * 100))
def buildModel(radiographs, resolutionLevels=5, maxLevelIterations=20, grayLevelModelSize=7, sampleAmount=3,
pcaComponents=25):
mouthLandmarks = [] # list of landmarks that contain all 8 teeth
for rad in radiographs:
mouthLandmark = Landmark(np.asarray([]), radiographFilename=None, toothNumber=-1)
mouthLandmark.radiograph = rad
for toothNumber, landmark in sorted(rad.landmarks.items(), key=lambda i: i[0]):
mouthLandmark.points = np.concatenate((mouthLandmark.points, landmark.points))
mouthLandmarks.append(mouthLandmark)
model = TeethActiveShapeModel(
mouthLandmarks=mouthLandmarks,
resolutionLevels=resolutionLevels,
maxLevelIterations=maxLevelIterations,
grayLevelModelSize=grayLevelModelSize,
sampleAmount=sampleAmount,
pcaComponents=pcaComponents
)
with util.Timer("Building multi resolution active shape model: Gray level models"):
model.buildGrayLevelModels()
with util.Timer("Building multi resolution active shape model: Procrustes analysis"):
model.doProcrustesAnalysis()
with util.Timer("Building multi resolution active shape model: PCA"):
model.doPCA()
return model
def predict_single(self, filename, clf_id, gpu_option='0'):
# TODO add a line of code to stack labels to create y_test, store in classifier
graph = tf.Graph()
probs = []
path = "./" + "_".join(
(self.tag, str(self.B), str(self.R), "time")) + ".out"
log = open(path, 'a')
predict_timer = util.Timer()
with graph.as_default():
# build input pipeline
labels, indices, values = self.load_sparse(filename, graph)
X = (indices, values)
y = labels
W = tf.constant(self.weights[clf_id])
b = tf.constant(self.bias[clf_id])
# build graph
y_p = tf.nn.softmax(matmul(X, W) + b)
init_op = tf.group(tf.global_variables_initializer(),
tf.local_variables_initializer())
# sess = tf.Session(config=tf.ConfigProto(
# allow_soft_placement=True
# ))
sess = None
if gpu_option == '1' or gpu_option == '0':
print("single gpu")
config = tf.ConfigProto()
config.gpu_options.visible_device_list = gpu_option
config.gpu_options.allow_growth = True
sess = tf.Session(config=config)
else:
sess = tf.Session()
sess.run(init_op)
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
try:
timer = util.Timer()
while not coord.should_stop():
probs.append(sess.run(y_p))
except tf.errors.OutOfRangeError:
print("Done predicting")
finally:
coord.request_stop()
coord.join(threads)
sess.close()
log.write("PREDICT B={} R={} time={}\n".format(
self.B, self.R, predict_timer.elapsed()))
log.close()
return np.concatenate(probs, axis=0)
def match(self, image):
dims = len(np.shape(image))
if dims == 3:
self.logger.info("Converting image to GRAY before matching")
image = cv2.cvtColor(image, cv2.COLOR_BGR2GRAY)
with util.Timer("extract corners"):
corners = util.get_corners(image, self._max_match_corners)
image = cv2.GaussianBlur(image, (7, 7), 25)
key_points_trained = []
key_points_matched = []
key_points_pairs = []
for corner in util.iter_timer(corners,
title="Matching corners",
print_iterations=False):
probs = np.zeros((self._classes_count, ))
patch = util.generate_patch(image, corner, self._patch_size)
for fern_idx, fern in enumerate(self._ferns):
k = fern.calculate(patch)
probs += self._fern_p[fern_idx, :, k]
most_probable_class = np.argmax(probs)
best_key_point = self.key_points[most_probable_class]
key_points_trained.append(best_key_point)
key_points_matched.append(corner)
key_points_pairs.append((best_key_point, corner))
return util.flip_points(key_points_trained), \
util.flip_points(key_points_matched), \
key_points_pairs
def run_tests(connection, iterations=1):
c = connection.cursor()
# Implicit tests
c.execute('SELECT target FROM targets')
res = c.fetchall()
test_urls = ['http://%s/' % (t[0]) for t in res]
logger.info('Running %d implicit tests, %d iterations' %
(len(test_urls), iterations))
# Explicit tests
c.execute('SELECT test FROM tests')
res = c.fetchall()
test_urls.append([t[0] for t in res])
logger.info('Running %d explicit tests, %d iterations' %
(len(res), iterations))
for i in range(0, iterations):
for test_url in test_urls:
timer = util.Timer()
timer.start_timer('Applying rules for %s' % test_url)
result_url = cache.cache.apply_rules(test_url)
timer.end_timer('Done. %s -> %s (took {.10f} sec)' %
(test_url, result_url))
c.close()
def update_network(self, minibatchs):
indices_all, priorities_all, losses = [], [], []
with util.Timer("Learner update:"):
for (indices, weights, samples) in minibatchs:
samples = [pickle.loads(lz4f.decompress(s)) for s in samples]
priorities, loss_info = self.update(weights, samples)
indices_all += indices
priorities_all += priorities
losses.append(loss_info)
current_weights = self.get_weights()
total_loss = sum([l[0] for l in losses]) / len(losses)
policy_loss = sum([l[1] for l in losses]) / len(losses)
value_loss = sum([l[2] for l in losses]) / len(losses)
reward_loss = sum([l[3] for l in losses]) / len(losses)
losses_mean = (total_loss, policy_loss, value_loss, reward_loss)
return (current_weights, indices_all, priorities_all, losses_mean)
def test_Timer(self):
sysout = StringIO()
with util.Timer('test', out=sysout):
pass
output = sysout.getvalue()
# not really much we can test for here, without being too brittle
assert output.startswith('test')
def remote_alias(self):
alias = None
try:
ns = int(self.NameSelect)
except Exception:
ns = -1
if 1 <= ns <= 3:
alias = [self.DisplayName, self.IMName, self.NickName][ns - 1]
if not alias:
# does this protocol have enough aliases?
alias = self.RealName or self.DisplayName or self.UserName or self.IMName or self.NickName
if not alias and not getattr(self, '_pending_info_request', False):
util.Timer(
common.pref('msim.contact_info.request_timeout',
type=int,
default=5),
lambda: setattr(self, '_pending_info_request', False)).start()
self._pending_info_request = True
self.protocol.request_buddy_info(self.id)
if isinstance(alias, bytes):
return alias.decode('utf8')
return alias
def next_file(self):
if self.cancelling:
return
if sys.DEV and not sys.opts.force_update:
self.unchecked_files = []
self.delete_files, self.update_files = dev_integrity_check(
self.local_dir)
self.files_processed()
return
if self.unchecked_files:
if self.fast_mode:
while self.fast_mode and self.unchecked_files and not self.cancelling:
self._check_file()
else:
self._check_file()
import common
interval = common.pref('digsby.updater.file_integrity_interval',
type=int,
default=0.01)
if interval == 0:
interval = 0.01
t = util.Timer(interval, self.next_file)
t._verbose = False
t.start()
else:
self.files_processed()
def queue_next_file(self):
interval = common.pref('digsby.updater.file_download_interval', type = int, default = 0.1)
if interval == 0:
interval = 0.1
t = util.Timer(interval, self.next_file)
t._verbose = False
t.start()
def set_timeout(self, msgobj):
timeout = getattr(msgobj, 'timeout', None)
if timeout is not None and common.pref(
'msn.socket.use_timeout', type=bool, default=False):
log.info('Starting timeout for %r', msgobj)
timer = util.Timer(timeout, self.timeout_handler(msgobj))
self.timeouts[msgobj.trid] = timer
timer.start()
def update_check_later(*a):
'''
The app performs an initial update check 5 minutes after launching.
(After that, it's every 6 hours - see UpdateManager.setup)
'''
util.Timer(
common.pref('digsby.updater.initial_delay', type=int, default=5 * 60),
update_check).start()
def reset(self):
self._success = False
self._failure = False
self._complete = False
self._signal = None
self._started = False
self._timer = util.Timer()
self._startFrame = None
def __init__(self, states):
if not states:
raise Exception("State machine can't be empty")
self.states = list(states)
self.istates = range(len(states))
self.initial = states[0]
self._timer = util.Timer()
self.transition(self.initial)
for i in range(len(states)):
setattr(self, states[i], i)
def deserialize(file: IO):
module_logger.info("Deserialiazing FernDetector from {}".format(
file.name))
version = int(file.readline().strip())
if version != 1:
msg = "Can't deserialize FernDetector from {}. Incorrect version of model. Expected 1, found {}"\
.format(file.name, version)
module_logger.error(msg)
raise AssertionError(msg)
num_ferns = int(file.readline().strip())
ph, pw = map(int, file.readline().strip().split(","))
with util.Timer("Deserializing ferns"):
ferns = [Fern.deserialize(file) for _ in range(num_ferns)]
fern_bits, max_train, max_match = map(
int,
file.readline().strip().split(","))
with util.Timer("Deserializing fern_p"):
F, C, K = map(int, file.readline().strip().split(","))
fern_p = np.zeros((F, C, K), dtype=float)
for fern_idx in range(F):
for class_idx in range(C):
line = list(map(float, file.readline().strip().split(",")))
fern_p[fern_idx, class_idx, :] = line
line = file.readline().strip().split(",")
key_points = list(util.grouper(map(int, line), 2))
module_logger.info("Creating FernDetector")
detector = FernDetector(patch_size=(ph, pw),
max_train_corners=max_train,
max_match_corners=max_match,
ferns=ferns,
ferns_p=fern_p,
classes_cnt=C,
key_points=key_points,
fern_bits=fern_bits)
module_logger.info("Deserialization complete.")
return detector
def merge_all():
mdf = pd.DataFrame()
num_per_run = get_num_per_run()
timer = util.Timer(total=num_jobs)
for start in range(0, len(fns), num_per_run):
end = start + num_per_run
df = pd.read_csv(out_dir + f'features-{start}-{end}.csv', index_col=0)
mdf = mdf.append(df)
timer.update()
mdf.to_csv(out_dir + 'features.csv')
return
def __init__(self,
dest=115 * core.DEG_T_RAD,
stepSize=26 * core.DEG_T_RAD,
skipFirstPause=False):
Task.__init__(self)
self.dest = dest
self.stepSize = stepSize
self.pauseTime = 0.2083
self.skipFirstPause = skipFirstPause
self.isPaused = True
self.timer = util.Timer()
def filter_and_save(name, all_data, mdf):
# Filter, then convert to dict
all_d = {}
print(f'Filtering {name} ...')
timer = util.Timer(total=len(mdf))
for idx, row in mdf.iterrows():
all_d[row['Name (unique)']] = all_data[row['Stepchart index']]
timer.update()
with open(out_dir + f'{name}.pkl', 'wb') as f:
pickle.dump(all_d, f)
return
def reset(self):
if not self._initializing:
self.trace("Reset")
self._started = False
self._finished = False
self._aborted = False
self._timer = util.Timer()
self._iterations = 0
self._frames = 0
for k, v in self._kwargs.iteritems():
if k == 'name': continue
setattr(self, k, v)
def leaveOneOutCrossValidation(radiographs, resolutionLevels,
maxLevelIterations, grayLevelModelSize,
sampleAmount, PCAComponents):
print("\nSTARTING LEAVE ONE OUT CROSS VALIDATION.\n")
accuracy = 0
precision = 0
recall = 0
mirroredRadiographs = [r for r in radiographs if r.mirrored]
radiographs = [r for r in radiographs if not r.mirrored]
for i in range(len(radiographs)):
trainSet = mirroredRadiographs + radiographs[:i] + radiographs[i + 1:]
testSet = [radiographs[i]]
with util.Timer(
"Building multi resolution active shape model, leaving radiograph {} out"
.format(i)):
model = MultiResolutionASM.buildModel(trainSet, resolutionLevels,
maxLevelIterations,
grayLevelModelSize,
sampleAmount, PCAComponents)
with util.Timer(
"Generating segmentation masks and comparing to ground truth".
format(i)):
gen = MaskGenerator(testSet[0], model)
acc, prec, rec = gen.doSearchAndCompareSegmentations()
print()
accuracy += acc
precision += prec
recall += rec
accuracy /= len(radiographs)
precision /= len(radiographs)
recall /= len(radiographs)
print("Averaged results after LOO cross-validation:")
print("Accuracy = {:.2f}%, Precision = {:.2f}%, Recall = {:.2f}%".format(
accuracy * 100, precision * 100, recall * 100))
def merge(start, end):
start, end = int(start), int(end)
sub_fns = fns[start:end]
timer = util.Timer(total=len(sub_fns))
mdf = pd.DataFrame()
for fn in sub_fns:
df = pd.read_csv(inp_dir + fn, index_col=0)
mdf = mdf.append(df)
timer.update()
mdf.to_csv(out_dir + f'features-{start}-{end}.csv')
return
def restart_and_update(tempdir):
'''
Registers _launch_updater as an atexit function, attempts to get the app to quit, and in the event the interpreter
is still running in 7 seconds, calls _launch_updater anyway.
Special care is also taken to make sure we're not still in the OnInit handler of the wxApp.
'''
import atexit
atexit.register(_launch_updater, tempdir)
force_restart_timer = util.Timer(7, _launch_updater, tempdir)
app = wx.GetApp()
# Don't call DigsbyCleanupAndQuit if we're not yet out of OnInit - the startup sequence will do it for us.
if app.IsMainLoopRunning() and app.DigsbyCleanupAndQuit():
force_restart_timer.start()
def encode_points_mtx_nd(self, pts_nd, axis=1, returnSparse=False):
t = util.Timer()
pts_flt = util.flatten_nd_array(pts_nd, axis=axis)
P = pts_flt.shape[0]
(dists, inds) = self.nbrs.kneighbors(pts_flt)
pts_enc_flt = np.zeros((P, self.K))
wts = np.exp(-dists**2 / (2 * self.sigma**2))
wts = wts / np.sum(wts, axis=1)[:, util.na()]
pts_enc_flt[np.arange(0, P, dtype='int')[:, util.na()], inds] = wts
pts_enc_nd = util.unflatten_2d_array(pts_enc_flt, pts_nd, axis=axis)
return pts_enc_nd
def multiResolutionSearch(self):
with util.Timer("Multi resolution search"):
self.setCurrentResolutionLevel(self.model.resolutionLevels)
self.initializeLandmark()
for level in range(self.model.resolutionLevels - 1, -1, -1):
self.setCurrentResolutionLevel(level)
self.drawLandMarkWithNormals(self.currentLandmark)
cv2.imshow(self.name, self.img)
cv2.waitKey(1)
self.currentLandmark = self.model.improveLandmarkForResolutionLevel(
resolutionLevel=level,
img=self.currentRadiograph.imgPyramid[level].copy(),
landmark=self.currentLandmark)
def __init__(self, *states):
if not states:
raise Exception("State machine can't be empty")
self.states = dict()
self.stateValues = set()
for i in range(len(states)):
state = states[i]
self.states[i] = state
self.stateValues.add(state)
setattr(self, state, i)
self.initial = states[0]
self.state = self.initial
self._timer = util.Timer()
self.debug = False
self.transition(self.initial)
def set_status_message(self, message, callback=None):
def on_error(e):
e_msg = getattr(e, "headers", {}).get("x-opensocial-error", e)
callback.error(e_msg)
self.update()
callback.success += lambda *a: util.Timer(2, self.update).start()
import hooks
callback.success += lambda *a: hooks.notify(
'digsby.myspace.status_updated', *a)
self.api.call('statusmood/@me/@self',
OpenSocial=True).PUT(data=json.dumps(
dict(status=message.encode('utf8'), moodName=None)),
retries=1,
success=callback.success,
error=on_error)
def sync_weights_and_rollout(self, current_weights, T):
#: 最新のネットワークに同期
if current_weights:
self.sync_weights(current_weights)
with util.Timer("Actor:"):
if self.lives == 0:
self.reset_env()
#: 1episodeのrollout
game_history = self.rollout(T)
samples, priorities = self.make_samples(game_history)
return self.pid, samples, priorities
def evaluate(self,
filename,
chunck_size=10000,
gpu_option='0',
load_probs=False):
P = None
if load_probs is False:
self.predict(filename, gpu_option=gpu_option)
path = "./" + "_".join((self.tag, str(self.B), str(self.R), "time")) + ".out"
log = open(path, 'a')
eval_timer = util.Timer()
P = self.get_complete_probs()
y_test = self.get_test_labels(filename, gpu_option=gpu_option)
k = self.num_classes
num_test = P[0].shape[0]
print("num_test", num_test)
size = chunck_size
print("start merging")
pool = ProcessPoolExecutor()
futures = []
for i in range(num_test // size):
x_batch = P[:, i*size:(i+1)*size, :]
y_batch = y_test[i*size:(i+1)*size]
futures.append(pool.submit(self.evaluate_chunck, i, x_batch, y_batch))
if (num_test // size) * size < num_test:
i = num_test // size
x_batch = P[:, i*size:, :]
y_batch = y_test[i*size:]
futures.append(pool.submit(self.evaluate_chunck, i, x_batch, y_batch))
wait(futures)
correct = 0
for fut in futures:
correct += fut.result()
print("total accuracy is", str(correct / num_test))
log.write("EVALUATE B={} R={} time={}\n".format(self.B, self.R,
eval_timer.elapsed()))
log.write("ACCURACY={}\n".format(correct / num_test))
log.close()
def decode(self, rdata, file=sys.stdout):
org_tokens = rdata.orgdata[0]
org_attrs = rdata.orgdata[1] if len(rdata.orgdata) > 1 else None
n_ins = len(org_tokens)
timer = util.Timer()
timer.start()
inputs = self.gen_inputs(rdata, evaluate=False)
self.decode_batch(*inputs,
org_tokens=org_tokens,
org_attrs=org_attrs,
file=file)
timer.stop()
print(
'Parsed %d sentences. Elapsed time: %.4f sec (total) / %.4f sec (per sentence)'
% (n_ins, timer.elapsed, timer.elapsed / n_ins),
file=sys.stderr)
def decode(self, rdata, file=sys.stdout):
n_ins = len(rdata.inputs[0])
org_tokens = rdata.orgdata[0]
timer = util.Timer()
timer.start()
for ids in trainer.batch_generator(n_ins,
batch_size=self.args.batch_size,
shuffle=False):
inputs = self.gen_inputs(rdata, ids, evaluate=False)
ot = [org_tokens[j] for j in ids]
self.decode_batch(*[inputs], org_tokens=ot, file=file)
timer.stop()
print(
'Parsed {} sentences. Elapsed time: {:.4f} sec (total) / {:.4f} sec (per sentence)'
.format(n_ins, timer.elapsed, timer.elapsed / n_ins),
file=sys.stderr)
